VMD-L Mailing List

From: Alberto Sergio Garay (sgaray_at_fbcb.unl.edu.ar)
Date: Fri Jun 26 2009 - 07:13:44 CDT

Dear all

I have a lipid bilayer trajectory and I'm trying to make some analysis
on some particular lipid which it is in the border of my unit cell. I
need to keep all the molecules which are close to my target lipid(but
in other periodic box) spatially closed, so that I can make my analysis.

I have tried to use the command "pbc wrap", but I think I'm not
understanding well how it works. So below I detail what I do, what the
result was and what I hoped. May be some of you can tell me what I'm
doing wrong.

1) I have selected (sel) my target residue (which it is in the border
of the box).
2) I run "pbc wrap -centersel $sel -all"
3) My residue remain at a border of a "new" box
I hoped that my residue appeared in the center of a new box, with all
the other molecules around it.

2') I also run "pbc wrap -centersel $sel -center origin -all" (the
default for -center is unitcell)
3') In this case my lipid appeared rounded by all the molecules. In
the new box the lipid bilayer appeared
inverted, i.e.: the water were in the middle of the box and the lipids
were pointing outside. I think that is not
a problem, isn`t it?

Could anyone tell me whether what I'm trying to do is posible? or I
need a more elaborated script to do so?
Could anyone explain me how the pbc wrap works?

Thank you in advance.

Sergio 

-- 
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221